## Error in library(future.apply) : 
##   there is no package called 'future.apply'

Project info

Samples: dcDNA Seq
pychopper: no
mapping version: v6
LoRTIA: yes (stranded only output)

Normalization: Viral read count

TES dynamics

Those reads were counted only, where the 3-prime adapters were “correct” (according to LoRTIA)

Statistics of counts

Difference from mean

Varcoeff

Clustering of samples

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The sample 48h_3 stands out!

Filtering of samples

Clustering of genes into de-novo clusters using hierarchial clustering

Cluster memberships

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Optimal number of clusters

Cut the tree at an optimal number of clusters

Clustering statistics: Cluster number: 5

## [1] "ORF27, ORF26, ORF25"          "ORF37, ORF36, ORF35, ORF35.5"
## [3] "ORF41, ORF42, OF43"           "ORF24"
## [1] 4

Clustering statistics: Cluster number: 6

## [1] "ORF27, ORF26, ORF25"          "ORF37, ORF36, ORF35, ORF35.5"
## [3] "ORF41, ORF42, OF43"           "ORF24"
## [1] 4

Clustering statistics: Cluster number: 7

## [1] "ORF27, ORF26, ORF25"          "ORF37, ORF36, ORF35, ORF35.5"
## [3] "ORF41, ORF42, OF43"
## [1] 3

Selected number of clusters: 7

## [1] "ORF27, ORF26, ORF25"          "ORF37, ORF36, ORF35, ORF35.5"
## [3] "ORF41, ORF42, OF43"
## [1] 3

Remove genes from clusters ?

## The following genes were removed from their corresponding clusters 
##            as their silhouette widths were lower than 0.1 and their distance from the group centroid was higher than 0.5: 
## ORF27, ORF26, ORF25
## ORF37, ORF36, ORF35, ORF35.5
## ORF41, ORF42, OF43

Assigning genes to clusters

Summarize and melt

Heatmaps

Normalized Expression

Expression delta ~ 6 hpi

Z-score of expression delta ~ 6 hpi

ORF kinetics, according to literature-based kinetic classes

Barplot of mean and SD

Figure 4 REVIEW - Mean and SD with linear connection

Mean and SD with loess function

Mean and SD with linear connection - Figure 4

Each replicate with loess

ORF kinetics, according to de-novo kinetic classes

Mean and SD with linear connection

Figure 5 REVIEW - Mean and SD with linear connection

Compare literature and de novo kinetic classes

Combined Kinetic classes

De Novo Clusters

Literature clusters